DNA and Genetic Genealogy May Unlock the Secret of Penny Doe’s Identity

| November 25, 2022

CLARION, Pa. (EYT) – Extracting DNA out of 32-year-old bones is tricky business. In order for DNA to survive, the right conditions must be present.

This is Part Three of an ongoing investigation into the identity of Clarion County’s “Penny Doe.” Please see our other articles in the series linked at the bottom of this article.

I talked to a geneticist about a year ago who told me that someone he knew was able to extract DNA from mammoth fur that was purchased from eBay. I figured that if DNA could be extracted from an arctic mammal that’s been extinct for some 4,000 years, then getting DNA from 32-year-old remains of a yet-to-be-identified woman wouldn’t be much of a problem. It turns out I may be wrong about that.

But, somebody out there knows Penny’s real name and probably wonders what happened to her. So, if I can, I want to use DNA to find that person. But, there are several steps that I need to go through in order to make that happen. And, as I’m learning, it’s actually a long shot. But, we’re going to take the shot, anyway.

mercyhurst_university_penny_doe_skeletonPenny Doe’s skeleton, curated by Dr. Dennis Dirkmaat at Mercyhurst University. Photograph was taken by Gavin Fish on September 6, 2022.

After my last story on this case, several people reached out to me from different organizations offering to help extract DNA from the bones that Dr. Dirkmaat has been curating at Mercyhurst University all these years.

From all the prospects, I selected two–one to extract the DNA and another to do the genotyping–and began the process of attempting to get Penny’s DNA. Both labs I chose asked to remain anonymous.

I reached out to Clarion County Coroner Dan Shingledecker shortly after I’d made my choice and asked him if he would be willing to request a sample of Penny Doe’s bones from Dr. Dirkmaat. He agreed, and a few days later, I received an email saying he had the sample. Then, we worked together to get the sample over to the first lab. I must say once again, Dan has been instrumental in helping me as I try to solve this mystery.

Once the sample was sent, I made the long drive from my home in Venango County to the lab (that remains anonymous) to meet with my genetics volunteer to watch them at work. But, to my surprise, I was asked to do the extraction myself.

Penny Doe Femur Fragment After DNA ExtractionThe fragment of Penny Doe’s femur after part of the bone was removed for DNA extraction. Photograph was taken by Gavin Fish on November 2, 2022.

I don’t want to exaggerate my part in this. I definitely don’t know what I’m doing. I was just the hands that did the work. It was all done under the supervision and instruction of a trained technician.

Step one was to pulverize some of the bone. Because bones are porous, as it was explained to me, DNA would most likely be intact inside the bone rather than on the surface. So, we took a common cordless drill and dug into the bone, leaving several small holes behind. The bone dust then fell onto a sanitized tray, where I collected it with a small spatula and put it into six small plastic tubes.

Buffer and Proteinase Being Added to Penny Doe's Bone Dust
Solution being added to tubes containing particles of Penny Doe’s bone. Photograph was taken by Gavin Fish on November 2, 2022.

From there, we added two solutions: one, called a buffer, and another which is called Proteinase K Solution. Then, the tubes went into an incubator for 24 hours which took the tubes up to 60 degrees Celsius, or 140 degrees Fahrenheit. This prepared Penny’s bone dust for DNA extraction and amplification; that process took another 48 hours or so.

Penny Doe's DNA in Tubes on Thermal CyclerDNA extraction solution being brought up to 60℃ Celsius. Photograph was taken by Gavin Fish on November 2, 2022.

Extraction is the process of removing the DNA from the other parts of the cells in Penny’s remains. Speaking as a layperson who really doesn’t understand what’s happening chemically, basically what happens in that solution at that temperature is the cells break down. Then, there’s a process of separating the DNA molecules from the cell fragments. Once you have pure DNA, you can move on to amplification.

Amplification is the process of making copies of the DNA you extracted.

It fascinates me that this is even possible to do in a lab. I mean, our bodies do it all the time. But, the fact that somebody figured out a way to do it on purpose just boggles the mind. And, that somebody was a chemist named Kary Mullis. He developed a process called polymerase chain reaction, or PCR. He actually won the Nobel Prize for Chemistry for this process.

This is how PCR works:

By heating DNA molecules above 90 degrees Celsius, or 194 Fahrenheit, their two strands are separated from one another. Then, by adding an enzyme to the solution that the DNA is suspended in–one that is present in our bodies all the time–the other side of the molecule is built onto each strand, leaving you with two exact copies of the original DNA molecule. Each time the solution is heated up above 90 degrees Celsius and then cooled off again, the quantity of DNA molecules in the solution doubles.

Now, this is a very basic explanation, reflecting my understanding of it. The part that blew my mind, though, is that the enzyme in our bodies that reads the strand of the DNA molecule and then builds on the other side can’t actually survive at 90 C. But, organisms that live in the deepest part of the ocean next to volcanic vents have enzymes that thrive above 90 C. And, it turns out their DNA is replicated in the same way ours is. So, scientists use the polymerase enzyme from those organisms to amplify human (and other) DNA in a lab.

Like I said, it’s mind-boggling.

So, getting back to the amplification cycle, each time the solution is heated and then cooled takes about five minutes. That means if you started with one DNA molecule, at the end of an hour, you would have 2,048 copies of the original molecule. And after two hours, you’d have 8,388,608. That’s the process that Penny’s DNA went through over 24 hours after I left the lab.

Two days later, I reached out to my volunteer to see if we’d been successful in extracting and amplifying Penny’s DNA, their answer was, “There wasn’t as much as I’d hoped, but I think I’ve amplified it enough for genotyping.”

With that, they sent the DNA to lab #2 (also remaining anonymous). From that point on, it was simply a waiting game.

In order to find out who Penny Doe is, we need to do something called “genetic genealogy.” This is the practice of finding people who share certain segments of her genetic code.

Penny_Doe_Clay_Mask_Mercyhurst_University This clay mask was created by reconstruction artist Michael Taister in April or May of 1991. Photograph was taken by Gavin Fish on September 6, 2022.

DNA is a molecule that is arranged in a helical ladder. We’ve all seen depictions of what it looks like, but we usually just see a small segment. In reality, each strand of our DNA is about six feet long and about 1/40,000th of the thickness of a human hair.

The rungs on the ladder are made up of a pair of what are called bases. There are only four different bases. They are called guanine, cytosine, adenine, and thymine. When mapping a genome, scientists take the first letter of each base, and write out the “genetic code” as a long word spelled-out using G, C, A, and T. And, when I say long, I mean long.

In the human genome, there are about three billion pairs of bases in our DNA. So, our genetic code is a word with about six billion letters. In all the human family, we share about 99.9% of the same genetic code. But, there are important segments in that code that we know tend to be different person to person.

So, what lab #2 has to do is break up the code into segments, then filter out the 99.9% of the code that we all share, leaving only the differences. Then, because that dataset is still too big at 30 million letters of code, they have to filter even more. In the end, they’ll produce a report that has between 300,000 and 600,000 letters of code and will send it back to me.

At that point, all of the lab work will be done, and I’ll be left to do the genetic genealogy—something I’ve never done before. This is the process of comparing the report I get back from lab #2 with reports from others who’ve uploaded their genetic information to public DNA databases.

Hopefully, we can find somebody who has a match for a few of the segments of Penny’s DNA, making them a genetic relative. And then, it’s all about following their genealogy to a common ancestor of Penny’s and working back down the family tree until we find the identity of Penny herself.

I love family history research, but I’ve never done anything like this before. The good news is, though, that I have a couple more volunteers waiting in the wings to help me on that part of my journey.

In Part Four of this series, I hope to be done with the genetic genealogy research, and may even know who Penny Doe is.

location_of_penny_does_remains_when_discoveredPenny Doe’s remains were found at this location by Angie Clinger and three other children, July 22, 1990. Photograph was taken by Gavin Fish on August 4, 2022.

The report below describing the discovery of “Penny Doe” was released sometime after May of 1991 by Pennsylvania State Police. Obtained by Gavin Fish on September 7, 2022, through a Right to Know Law Request.

Penny_Doe_News_Release_1991

This is Part Three of an ongoing investigation into the identity of Clarion County’s “Penny Doe.”

Please see our other articles in the series:

  1. Part One: For 32 Years, Someone in Clarion County Has Kept a Horrifying Secret
  2. Part Two: New Information Uncovered in Penny Doe Case for the First Time in 30 Years

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Category: Local News, News, Regional News

Gavin Fish is a reporter for EYT Media Group and YouTuber based in Venango County. In addition to his YouTube Channel, he has contributed to investigations and reports for ABC News, Investigation Discovery, and Fox Nation, and has collaborated on projects developed for Netflix, Oxygen, Discovery Channel, Amazon Prime, and Hulu.
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